Effects of preanalytical sample collection and handling on comprehensive metabolite measurements in human urine biospecimens

Authors: BRAISTED, JOHN - National Institutes Of Health (NIH); Henderson, Theresa; Newman, John; MOORE, STEVE - National Institutes Of Health (NIH); SAMPSON, JOSHUA - National Institutes Of Health (NIH); MCCLAIN, KATHLEEN - National Institutes Of Health (NIH); ROSS, SHARON - National Institutes Of Health (NIH); Baer, David; MATHE, EWY - National Institutes Of Health (NIH); ZANETTI, KRISTA - National Institutes Of Health (NIH)

Submitted to: American Journal of Epidemiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/30/2024
Publication Date: N/A
Citation: N/A

Interpretive Summary: Over the last decade, there has been an increase in the use of epidemiologic studies using metabolomics to examine the role of metabolism in health and disease and to identify biomarkers. With the growing interest in using metabolomics in these studies, there have been efforts to understand how preanalytical factors (for example, the collection, shipment, storage (temperature and duration), and handling (e.g., aliquoting)) affect findings. Urine samples from 13 study participants were collected and the samples were subjected to various handling conditions commonly encountered in practice (borate, chlorhexidine, or no urine preservative, refrigeration time, and number/temperature of thaws) and examined how each condition affected observed circulating levels of over 1,000 metabolites. Results from this study highlight two key findings: 1) urine is strikingly less susceptible to sample handling effects than serum (research previously published); and 2) preservatives have the largest impact compared to refrigeration and freeze-thaw conditions. This study confirms the importance of implementing consistent handling conditions in epidemiological studies.

Technical Abstract: Epidemiology studies evaluate associations between the metabolome and disease risk. Urine is a common biospecimen used for such studies due to its wide availability and non-invasive collection procedure. Evaluating the robustness of urinary metabolomic profiles under varying preanalytical conditions is thus of particular interest. Here we evaluate the impact of sample handling conditions on urine metabolome profiles relative to the gold standard condition (no preservative, no refrigeration storage, single freeze thaw). Conditions tested included the use of borate or chlorhexidine preservatives, various storage and thawing conditions, and freeze/thaw cycles. Urine from 13 healthy participants yielded measurements of 1,048 metabolites for evaluation. We demonstrate that all sample handling conditions impact metabolite levels, with preservatives, particularly borate, showing the largest impact. When simulating a case-control study, we show that predicted changes in sample handling conditions impact metabolite levels. Finally, we demonstrate that sample handling-dependent impacts on the urinary metabolome are markedly smaller than those observed in serum. Overall, while changes in urine metabolites incurred by sample handling conditions are generally small, we recommend tracking and implementing consistent handling conditions and evaluating robustness of metabolite measurements for those showing significant associations with disease outcomes.